Links between diet and human disease, and between reactive species and disease, are so commonly considered as to lie in the realm of textbooks and the popular press. Links between mitochondria and energy production are generally appreciated by junior high school. Links between mitochondria and calcium (including signaling), free radicals, or cell death may be less known to the general public, but each has in excess of 10,000 PubMed citations. However, despite broad and strong theoretical considerations supporting casual connections between diet effects on mitochondria and diet effects on disease - and some specific experimental support - there are, to our knowledge, no systematic studies that bridge this fundamental gap. Bridging this gap is central to understanding environment-gene interactions, as suboptimal dietary macronutrient choices are arguably the major environmental stressor in individuals living in Western societies. We therefore propose to bridge this gap using an interdisciplinary, product-development approach to discover and confirm innovative plasma metabolomic and proteomic biomarkers for dietary intake of subclasses of fats and carbohydrates, and for their effects on mitochondrial (dys)function. We will then validate these markers by using them to test the hypothesis that diet-associated effects on mitochondria are linked to diet-associated changes in disease risk. Five Aims are proposed. Aim 1 To determine the effects of dietary changes in fatty acid and carbohydrate composition on mitochondrial physiology Aim 2 To determine the effects of dietary changes in fatty acid and carbohydrate composition on the plasma metabolome and proteome Aims 3 and 4: To determine the extent to which adherence to/presence of each diet, dietary constituent, and mitochondrial property predict type II diabetes (Aim 3) and breast cancer (Aim 4) in previously profiled case control studies nested within the Nurses'Health Study Aim 5: To provide an electronic archive of the metabolomic and proteomic constituents of the blood of participants that could be repeatedly mined for future testing of new hypotheses. The proposed studies are directly responsive to the RFA and further general NIH goals of focusing on health and early interventions rather than late stage disease.